Breeders have focused on yellow-seeded Brassica napus (rapeseed) for its better quality com- pared with the black-seeded variety. Moreover, flavonoids have been associated with this kind of rapeseed. In this study, we applied lipid chromatography-electrospray ionization mass spec- trometry (LC-ESI-MSn ) to compare flavonoids in developing seeds of natural black-seeded B. na- pus and yellow-seeded introgression lines selected from progenies of B. napus-Sinapis alba so- matic hybrids. Aside from the most abundant phenolic compounds (sinapine and sinapic acid) and 1, 2-disinapoylglucose, 16 different flavonoids were identified and quantified, including (-)- epicatechin, five monocharged oligomers of (-)-epicatechin ([DP 2]- , [DP 3]- , [DP 4] [DP 2]- B2 and [DP 2]- B5), quercetin, kaempferol, isorhamnetin-dihexoside, kaempferol-sinapoyl-trihexoside, isorhamnetin- sinapoyl-trihexoside, isorhamnetin-hexoside-sulfate, and isorhamnetin-3-O-glucoside. Most of the flavonoids accumulated with seed development, whereas some rapidly decreased during maturation. The content of these flavonoids was lower in the yellow-seeded materials than in the black seeds. In addition, variations of insoluble procyanidin oligomers and soluble phenolic acids were observed among both rapeseed varieties. Transcriptome changes of genes participating in the flavonoid pathway were discovered by quantitative reverse transcription polymerase chain reaction analysis. Consistent with flavonoid changes identified by high performance liquid chromatography analysis, the expression of most genes in the flavonoid biosynthetic pathway was also downregulated. Breeders have focused on yellow-seeded Brassica napus (rapeseed) for its better quality com- pared with the black-seeded variety. Moreover, flavonoids have been associated with this kind of rapeseed. In this study, we applied lipid chromatography-electrospray ionization mass spec-trometry (LC-ESI-MSn) to compare flavonoids in developing seeds of natural black-seeded B. na- pus and yellow-seeded introgression lines selected from progenies of B. napus-Sinapis alba so- matic hybrids. Aside from the The most abundant phenolic compounds (sinapine and sinapic acid) and 1, 2-disinapoylglucose, 16 different flavonoids were identified and quantified including (-) - epicatechin, five monocharged oligomers of (-) - epicatechin ([DP 2] Quercetin, kaempferol, isorhamnetin-dihexoside, kaempferol-sinapoyl-trihexoside, isorhamnetin-sinapoyl-trihexoside, isorhamnetin-hexoside-sulfate, and [DP2] isorhamnetin-3-O-glucoside. Most of the flavonoids accumulated with se ed development, while some finingly during maturation. The content of these flavonoids was lower in the yellow-seeded materials than in the black seeds. In addition, variations of insoluble procyanidin oligomers and soluble phenolic acids were observed among both rapeseed varieties. Transcriptome changes of genes participating in the flavonoid pathway were discovered by quantitative reverse transcription polymerase chain reaction analysis. Consistent with flavonoid changes identified by high performance liquid chromatography analysis, the expression of most genes in the flavonoid biosynthetic pathway was also downregulated.